将分子动力学模拟数据带入视野。

Bringing Molecular Dynamics Simulation Data into View.

机构信息

Institute for Medical Physics and Biophysics, Leipzig University, 04107 Leipzig, Germany; Institute for Medical Physics and Biophysics, Charité - Universitätsmedizin, 10117 Berlin, Germany; Berlin Insitute of Health (BIH), 10178 Berlin, Germany.

RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, CA, USA.

出版信息

Trends Biochem Sci. 2019 Nov;44(11):902-913. doi: 10.1016/j.tibs.2019.06.004. Epub 2019 Jul 10.

DOI:10.1016/j.tibs.2019.06.004

PMID:31301982

Abstract

Molecular dynamics (MD) simulations monitor time-resolved motions of macromolecules. While visualization of MD trajectories allows an instant and intuitive understanding of dynamics and function, so far mainly static representations are provided in the published literature. Recent advances in browser technology may allow for the sharing of trajectories through interactive visualization on the web. We believe that providing intuitive and interactive visualization, along with related protocols and analysis data, promotes understanding, reliability, and reusability of MD simulations. Existing barriers for sharing MD simulations are discussed and emerging solutions are highlighted. We predict that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.

摘要

分子动力学（MD）模拟监测生物大分子的时间分辨运动。虽然 MD 轨迹的可视化可以即时直观地了解动力学和功能，但迄今为止，发表的文献中主要提供静态表示。浏览器技术的最新进展可能允许通过网络上的交互式可视化共享轨迹。我们相信，提供直观和交互式的可视化以及相关协议和分析数据，将促进 MD 模拟的理解、可靠性和可重复性。讨论了共享 MD 模拟的现有障碍，并强调了新兴解决方案。我们预测，MD 轨迹的交互式可视化将很快被研究人员、研究联盟、期刊和资助机构采用，通过网络收集和分发 MD 模拟的结果。